Markers + reference

Coronilla

2 species · Fabaceae · Fabales

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Species 2
Genome length 150–150 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 676 0.0090 0.98 60.2 yes View details
trnL-UAA-trnT-UGU LSC 917 0.0135 0.97 67.3 yes View details
trnG-GCC-psbZ LSC 624 0.0065 0.99 49.7 yes View details
petN-trnC-GCA LSC 712 0.0084 1.00 54.6 yes View details
trnG-UCC-trnS-GCU LSC 786 0.0104 0.98 54.5 yes View details
psaI-pafII LSC 243 0.0207 0.99 57.1 yes View details
petA-psbJ LSC 817 0.0110 1.00 58.9 yes View details
trnP-UGG-psaJ LSC 692 0.0059 0.98 63.8 yes View details
ycf1 IRb 546 0.0000 1.00 31.3 no View details
ndhD SSC 1494 0.0013 1.00 48.7 yes View details
ycf1 SSC 5391 0.0082 1.00 42.8 yes View details
ndhD-psaC SSC 135 0.0370 1.00 73.8 yes View details
clpP1-psbB LSC 491 0.0042 0.96 62.6 yes View details
infA-rps8 LSC 114 0.0175 1.00 62.6 yes View details
trnE-UUC-trnY-GUA LSC 58 0.0172 1.00 62.4 yes View details
psbD-trnT-GGU LSC 834 0.0060 1.00 62.2 yes View details
atpH-atpF LSC 527 0.0076 1.00 61.8 yes View details
psaJ-rpl33 LSC 392 0.0104 0.98 61.8 yes View details
accD-psaI LSC 166 0.0301 1.00 61.6 yes View details
psbK-trnQ-UUG LSC 564 0.0054 0.98 61.2 yes View details
rpl2-trnH-GUG IRa 112 0.0179 1.00 60.7 no View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AAAGCCGAGTACTCTACCGT AGTCCTGAATTAGCTGCTGC 773–785 1.000 80.2
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AAGCCGAGTACTCTACCGTT AGTCCTGAATTAGCTGCTGC 772–784 1.000 80.2
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AAGCCGAGTACTCTACCGTT AATTATCCGTGAAGCGTGCA 797–809 1.000 78.3
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AAGCCGAGTACTCTACCGTT ATTATCCGTGAAGCGTGCAA 796–808 1.000 78.3
trnK-UUU-rbcL_p5 trnK-UUU-rbcL AAGCCGAGTACTCTACCGTT TATCCGTGAAGCGTGCAAAT 794–806 1.000 78.3
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 960–968 1.000 82.4
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 968–976 1.000 81.8
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 992–1000 1.000 81.4
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1000–1008 1.000 80.9
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 974–982 1.000 80.5
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTTGTTTTTCGACCGGAAG CAACCACTCAGCCATCTCTC 1769–1771 1.000 80.7
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTTGTTTTTCGACCGGAAG TGAGAAAACCCTCCCTCCAT 1502–1504 1.000 80.6
trnG-GCC-psbZ_p3 trnG-GCC-psbZ GGGTAGAGCAACTTGGTAGC CAACCACTCAGCCATCTCTC 1484–1488 1.000 80.5
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CCGTCTCCGCAACATTTTTC CAACCACTCAGCCATCTCTC 1426–1430 1.000 80.4
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CTTGAGGTCACGGGTTCAAA CAACCACTCAGCCATCTCTC 1448–1452 1.000 80.4
psbD-trnT-GGU_p1 psbD-trnT-GGU GAAACGGTCCCTACGTAACC GGCGTAAGTCATCGGTTCAA 954–959 1.000 78.1
psbD-trnT-GGU_p2 psbD-trnT-GGU GAAACGGTCCCTACGTAACC CCCCTTTAACTCAGCGGTAG 990–995 1.000 77.9
psbD-trnT-GGU_p3 psbD-trnT-GGU GAAACGGTCCCTACGTAACC TGAATCAAATGTGGCCCCTT 1004–1009 1.000 77.8
psbD-trnT-GGU_p4 psbD-trnT-GGU GAAACGGTCCCTACGTAACC TTGAATCAAATGTGGCCCCT 1005–1010 1.000 77.8
psbD-trnT-GGU_p5 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GGCGTAAGTCATCGGTTCAA 963–968 1.000 76.8
trnE-UUC-trnY-GUA_p1 trnE-UUC-trnY-GUA AAGTATGCCCCCATCGTCTA GATCAGCAAATTTGTGGGCC 237 1.000 79.4
trnE-UUC-trnY-GUA_p2 trnE-UUC-trnY-GUA AAGTATGCCCCCATCGTCTA GGATCAGCAAATTTGTGGGC 238 1.000 79.4
trnE-UUC-trnY-GUA_p3 trnE-UUC-trnY-GUA AAGTATGCCCCCATCGTCTA CATGTCATGGTGGATCAGCA 249 1.000 79.2
trnE-UUC-trnY-GUA_p4 trnE-UUC-trnY-GUA TCTCTTTCAAGGAGGCAACG GATCAGCAAATTTGTGGGCC 202 1.000 78.9
trnE-UUC-trnY-GUA_p5 trnE-UUC-trnY-GUA TCTCTTTCAAGGAGGCAACG GGATCAGCAAATTTGTGGGC 203 1.000 78.9
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAGGCAAGACTTACTA TTTCCCCAGTTCAAATCCGG 768–770 1.000 79.6
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAGGCAAGACTTACTA TTTATCGTTTTGGCGGCATG 821–823 1.000 78.0
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAGGCAAGACTTACTA GGGGGACTGCAAATCCTTTT 786–788 1.000 77.4
petN-trnC-GCA_p4 petN-trnC-GCA TCTTCCCCATACTACGAGGG TTTCCCCAGTTCAAATCCGG 819–821 1.000 76.9
petN-trnC-GCA_p5 petN-trnC-GCA TACCATTAAAGCAGCCCAGG TTTCCCCAGTTCAAATCCGG 780–782 1.000 76.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Coronilla vaginalis PP190945.1 150098 View on NCBI ↗
Coronilla valentina subsp. glauca ON009080.1 149868 View on NCBI ↗